Fields, Christopher J | 4 Dec 22:10 2012

Re: Slowness of Bioperl with GFF3 database access


On Dec 4, 2012, at 2:53 PM, Adam Sj√łgren <asjo <at> koldfront.dk>
 wrote:

> On Wed, 28 Nov 2012 02:27:16 -0800 (PST), Francesco wrote:
> 
>> I'm experiencing that when I have to do a lot of accessess on a GFF
>> database (with Bio:DB::SeqFeature::Store) the slowness increase until
>> my script can stay running for more than a day.
> 
> First you'll need to find out what/where exactly it is slow. One way to
> do so is using a a profiler; this is a good one for Perl:
> 
> * https://metacpan.org/module/Devel::NYTProf
> 
> If you want more specific suggestions, you'll probably have to provide
> more information.
> 
> 
>  Good luck!
> 
>    Adam

If anything, we need more profiling of Bioperl code.  Ah, if we only had infinite time... :)

chris

Gmane